Redemption of the Soul
by Cain Loasa
Summary: Three months after Alice appears a war breaks out after Twilight Sparkle and Spike are killed, but as the group in plunged deeper into the war what if the people behind the war were always around them pulling the strings from the background.
1. Chapter 1

Applejack was walking through the apple orchard after the yearly harvest when she heard one of the trees start to rustle. She bucked the tree and the pony from the tree slammed heavily into the ground. The pony was white with a golden mane, and she was bruised a little bit. The pony slowly got to their feet but then they collapsed again.

"I'll go get help." Applejack told the pony before she galloped off.

When she got to the house she ran up to Big Mac.

"Big Mac, I need your help." Applejack replied.

"Eeyup, lead the way." Big Mac replied.

Applejack and Big Mac rushed back to the apple orchard but when they got to where the pony used to be; but when they got there the pony was gone.

"There was a pony here, right here." Applejack told him standing right in the spot where the pony had landed.

"I believe ya sis." Big Mac replied. "Now there ain't no pony here."

Applejack looked around and pulled her hat down.

"I'm going to town." Applejack replied as she walked off.

When Applejack got to town Rainbow Dash came running up to her.

"Did you see her?" Rainbow Dash asked her.

"Did I see who?" Applejack asked her.

"There was this one pony running through town, she was bruised a little bit and she ran straight into me." Rainbow Dash replied.

"Was she white with a golden mane?" Applejack asked her.

"Yeah, why?" Rainbow Dash asked her.

"She was up in one of the apple trees and I bucked her down." Applejack replied. "When I got back to where she fell she was gone."

"Strange, she plowed right into me and continued through town like I wasn't even there." Rainbow Dash replied.

Two stallions walked up to Applejack and Rainbow Dash and one showed them a picture of the mare they had been talking about.

"Have either you seen this mare?" The second stallion asked them.

"Nope, never seen her in my life." Rainbow Dash replied as Applejack quickly shook her head.

The two stallions looked them over before walking off and questioning another pony. Once they were out of earshot Applejack quickly turned to Rainbow Dash.

"We have to find her first." Applejack replied.

"Yeah, I was thinking the same thing, should we tell the others first?" Rainbow Dash asked her.

"No, not yet." Applejack replied. "We need to be able to vouch one way or the other."

"How would we know who is telling the truth or not?" Rainbow Dash asked her.

"We'll have to go with our guts on this one." Applejack replied.

"I'll look for her from the sky." Rainbow Dash replied.

"I'll look around the farm, she shouldn't have been able to get that far with her injuries." Applejack replied.

Rainbow Dash nodded before shooting into the sky as Applejack galloped back to the farm and almost ran into Big Mac.

"Where you going so quickly?" Big Mac asked her.

"I'm going to look for that mare, where are you going?" Applejack asked him.

"I'm going to visit Ms. Fluttershy." Big Mac replied.

"Make sure to give her one of the pies I made with Applebloom." Applejack replied.

"Eeyup." Big Mac told her before trotting off.

Applejack walked through the apple orchard listen intently for any sounds or movements in the trees. She was going to walk by the barn until she was Applebloom trying sneak out of it.

"Applebloom, what the hay are you up to?" Applejack asked her.

Applebloom just stopped and her head drooped as she walked back into the barn with Applejack following her.


	2. Chapter 2

"I'm sorry ma'am she spotted me." Applebloom told someone.

"It's okay child, we all make mistakes." A voice replied.

"Even you?" Applebloom asked the voice.

"Yes, even I make mistakes." The voice replied.

Applejack went closer to the corner where the voice was and she gasped when she saw the white mare laying on a pile of hay. She actually felt smaller as the mare's piercing emerald colored eyes focused on her. Then Applejack noticed the gash on the mare's shoulder that was still bleeding slightly. The mare glanced over at a hole in the wall of the barn with a piece of wood pointing downwards.

"Don't worry about the wall." Applejack replied. "Did you give her anything to eat Applebloom?"

"No, she said that would be her stealing from us." Applebloom replied.

"It ain't a problem." Applejack replied as she grabbed a basket of apples in her mouth.

Applejack set the basket of apples down beside the mare but she didn't make a move towards it.

"Can you lift your head?" Applejack asked her.

The mare barely had any strength to shake her head.

"Applebloom, go get Fluttershy and Big Mac, and don't talk to any stallions in suits." Applejack told her. "If you run into one and he asks you a question about this mare just deny everything."

Applebloom nodded before galloping off towards Fluttershy's place. Applejack laid down beside the mare and nuzzled her neck with her nose.

"Why are you helping me?" The mare asked her.

"I can make my own decisions can't I?" Applejack asked her.

Applejack grabbed one of the apples in her mouth and nudged it towards the mare who slowly took a bite out of it. She swallowed the bite painfully and looked away from Applejack.

"This shouldn't have happened." The mare replied.

The mare tried to stand up but she fell heavily onto her injured shoulder.

"Calm down, you'll make your injury worse." Applejack replied. "There are stallions after you, why?"

The mare's eyes widened and started to freak out and tried to stand again but Applejack touched her uninjured shoulder gently.

"Woah there, I didn't tell them anything." Applejack replied. "What is your name?"

The mare looked at Applejack and let out a pained breath.

"My name is Alice." Alice replied with a sigh.

"Now, how did you end up here?" Applejack asked her.

"I don't know." Alice replied. "Alice isn't even my real name, it's the one they gave to me."

"Who, the stallions?" Applejack asked her.

"Them and the researchers." Alice replied.

"Do you remember anything?" Applejack asked her.

Alice just shook her head as the barn door started to open up. She stared at the front of the barn as Big Mac and Fluttershy walked in behind Applebloom. When Fluttershy's eyes fell upon Alice she gasped as Big Mac walked over to Applejack. Alice tried to back away but she eventually stopped when the pain was unbearable.

"It's all okay darling." Fluttershy told her.

"So she was in the barn this whole time?" Big Mac asked her.

"I wonder how she got in here in the first place." Fluttershy told them. "The bruises all over her body would make it almost impossible for her to move without a unbearable amount of pain, and now with that gash in her shoulder she won't be able to move until that heals up."

"No, I have to leave, as in now." Alice replied as she struggled to her feet.

Big Mac eased himself under her and lifted her off the ground.

"As long as you're at this house your hooves won't touch the ground." Big Mac replied.

Before anyone could react Alice shot into the air at about five feet and then slammed into the ground. Big Mac walked over and lifted her up again.

"Could you not do that again?" Big Mac asked her.

Alice huffed as she rest her head against Big Mac's back.

"It's not possible even if I tried." Alice replied as Big Mac walked towards the house.

"What do ya mean?" Applejack asked her.

"What I did should've of been impossible since I'm an ordinary pony." Alice replied. "I shouldn't have the ability to use magic in the first place."

"So how do you do it?" Fluttershy asked her.

"It's what they did to me." Alice replied.

"Who are 'they'?" Big Mac asked her.

"I don't want to talk about it." Alice replied.

Fluttershy was about to press the matter but Big Mac just looked at her.

"I understand that you are all curious about who I'm and how I got here." Alice told them. "I don't know anything about myself as it is."

Fluttershy trotted up beside her and gently touched her shoulder.

"If you need anypony to talk to, I'll listen." Fluttershy told her.

"Thanks, I'll try to remember that." Alice replied before she blacked out.

Alice shot up her body soaked in sweat and her shoulder bandaged up. Big Mac walked into the room and sat down in front of her.

"It was sure a pain to bandage up your shoulder, with you bucking and all." Big Mac replied.

Alice noticed the hoof mark on Big Mac's shoulder.

"I'm about bucking at you." Alice told him quietly.

"Not a problem, you have pretty good aim for an unconscious pony." Big Mac replied.

"I've had practice." Alice replied as she rolled off the couch.

Big Mac was about to rush to her side but with one look he didn't move another inch.

"Sheesh, and I though that only a glare from Ms. Fluttershy could stop me cold." Big Mac replied.

Alice slowly made her way to the kitchen door where she smelled apple pies and a few fritters. Big Mac rushed forward and pushed the door open for her and she whispered something.

"What was that Ms. Alice?" He asked her.

"Just tell her how you feel." Alice replied.

"It's not that easy." Big Mac replied.

"You're easily one of the strongest stallions I know, and you're afraid to tell one mare how you feel?" Alice asked him.

Big Mac was about to speak when Fluttershy walked into the kitchen and his eyes focused on her.  
>"Something you want to tell her?" Alice asked him.<p>

Big Mac looked from Alice to Fluttershy and took a deep breath.

"You look very pretty today Ms. Fluttershy." Big Mac told her.

Fluttershy blushed deeply before she spoke, quieter than usual. "T-thank you, Big Mac, you look nice today as well."

Alice huffed before leaving the kitchen and she almost left the house when she saw Applebloom staring at her.

"What's up kid?" Alice asked her.

Applebloom didn't say anything just ushered her closer. When Alice got to her level Applebloom quickly braided and tied back her mane.

"What was all that about?" Alice asked her.

"Last night you were crying in your sleep, and when my big sis had given that ribbon she told me it would keep away any nightmares." Applebloom replied. "You need it more than me."

Alice hugged Applebloom tightly and failed to hold back tears as she hugged her back. When they separated Alice forced herself to smile.

"Where's your sister?" Alice asked her.

"She's in the orchard." Applebloom replied. "Follow me."

Alice fell in behind Applebloom who easily lead her through the orchard but Alice sensed something was wrong.

"Applebloom get down!" Alice yelled.

Applebloom wasn't even able to react before Alice pushed her to the ground. An arrow buried deep into a tree millimeters from Alice's face. Two stallions in suits walked out of the bushes with a tied up Applejack in between then, her face and body bruised and bloody.

"Come with us and no one will get hurt." One of the stallions told her.

"I know you aren't telling the truth, you always say that and then I'd loss every mental connection I had with them." Alice yelled as her eyes started to glow a neon green. "I'm sick of it."

Suddenly the two stallions dropped dead that instantly and the binding and gag on Applejack disappeared. Applebloom ran up to Applejack as Alice just stared vacantly into the distance.

"Applejack are you okay?" Applebloom asked her.

"Yeah, I'm just fine, I'll just have to heal." Applejack replied.

Suddenly Alice was lifting Applejack onto her back before she could protest.

"What 'bout your shoulder?" Applejack asked her.

"What I did to kill those two stallions, it also healed my shoulder." Alice replied.

Applejack rested her head on Alice's shoulder and looked at the setting sun.

"It sure is pretty." Applejack told her.

"You are too." Alice replied.

"What?" Applejack replied.

"I said think it's pretty too." Alice replied quickly.

Alice heard Applebloom snicker slightly and she glared at the filly. When they got to the house Fluttershy rushed forward and guided Alice to Applejack room where she gently laid her onto the bed.

"Could you go fetch some water and a few towels?" Fluttershy asked her.

Alice vanished and quickly reappeared with a few buckets of water and five towels, but sweat coated her face.

"Whatever I did back in the orchard unlocked some of my magical potential." Alice told them when she saw Applejack and Fluttershy's shocked expressions.

"Just help me wash all this blood off of Applejack's body." Fluttershy replied.


	3. Chapter 3

Washing all the blood off of Applejack took an hour and a half due to the amount dried in her mane and tail, but by the time Fluttershy and Alice were done they were both sweating, with Applejack having fallen asleep awhile into it. Then Fluttershy quickly bandaged Applejack's left back leg and pulled Alice out of the room.

"Alice, can I talk to you about something?" Fluttershy asked her.

"Sure, what's on your mind?" Alice asked her.

"I like Big Mac but I don't want to ruin the friendship I have with him if he doesn't like me." Fluttershy replied.

Alice barely held back a chuckle as Fluttershy told her this.

"Have you made this apparent?" Alice asked her.

"A couple of times." Fluttershy replied.

"Then, my dear Fluttershy you two are completely oblivious to each other feelings for each other." Alice replied. "Just tell him."

With that Alice reentered Applejack's room leaving Fluttershy to wonder what to do.

Applejack shot up in her bed and looked over the side to find Alice curled up at the side of her bed. She also noticed that her left back was bandaged up and finally noticed a bell by her bed. Applejack touched it to where it barely rang and Alice shot to her feet.

"You're awake." Alice responded, a look of relief passing over her face.

"Yeah, how long was I asleep?" Applejack asked her.

"About three months." Alice replied.

"I smell like Wionna after she ran through the mud a couple of time." Applejack replied as she smelled herself. "What's up with my leg?"

"After the swelling had gone down enough to where Fluttershy could tell that it's shattered." Alice replied.

"How am I going to get clean?" Applejack asked her.

"I'm leaving that to Shy; I have to go scouting around with the group to find anymore encampments." Alice replied as she pulled on a cloak.

That was when Applejack noticed the a bunch of scars on Alice's left side.

"What happened when I was out?" Applejack replied.

"Again, I'm going to have to leave that to Shy." Alice replied before she left.

When Fluttershy entered the room with a bucket of soapy water and a sponge Applejack instantly started questioning her.

"What's up with Alice?"

Soon Alice was soaring through the sky on wings of pure light with Rainbow Dash and Derpy, she was carrying Vinyl Scratch and Derpy was carrying Dr. Whooves.

"Whooves, do you have an enemy count and main concentration?" Alice asked him.

"The big building off to the left seems to be a shanty form of their town hall." Dr. Whooves replied while pointing to the building.

"Ready Dash, Vinyl?" Alice asked them.

They both nodded as before Vinyl tossed Rainbow Dash two live bass grenades which she shot down and dropped them down the chimney of the large building. She was well out of range when they went off blasting three large holes each in the building as the group landed.

"Where is the injection located?" Vinyl asked Alice.

"Shack 45 paces away and 13 to the right." Alice replied. "Hand me the PBC."

Vinyl sadly handed her the PBC, or Portable Bass Cannon, and quickly set up her turn tables.

"Everypony ready for the attack?" Alice asked them as the PBC sound cord connected to her back and upper right arm.

They all nodded in unison and Alice glanced at the robotic cord on Derpy's neck. It calmed her down and focused her but never had they put it under this sort of pressure, but Dr. Whooves reassured her that it wouldn't short circuit. Alice gritted her teeth as the PBC started to power up from the noise from Vinyl's turn table and she slipped on the sunglasses that Vinyl had provided her. She took a deep breath as the Bass Cannon reached full power and the Hetrarian Squads started their attack.

"See you later." Alice replied.

She let out her breath and fired the Bass Cannon into the shack and smiled as it exploded in a blue mushroom cloud. The Bass Cannon shrunk into a smaller version of itself which Alice tossed to Vinyl who instantly started to fire it going back to back with Rainbow Dash and joined in on the string of insults that Dash was dishing out. So far all of their missions had been a success, five in total, but they were all feeling the effect of stress and the injection that rained down on them at every mission.

"Everyone get ready." Alice yelled.

Rainbow Dash grabbed Vinyl Scratch and Derpy grabbed Dr. Whooves and they both launched up to where every enemy was focused on Alice who was still running on the ground at her fastest, clearing 3 yards per second. She shot upwards and everyone in the air saw what they were all trying to hide, an outline formed around Alice; a humanistic one, before she shot to the ground. When Alice hit the ground the enemies were either pummeled to death by debris or baked alive by the sudden heat wave. She was back in the air leading the group back to Ponyville towards the library to report their progress to Celestia and Luna.

"You're getting better at it." Rarity replied.

"I'm getting better at what?" Alice asked her.

"Other than leading the current group and unconsciously recruiting more ponies to the cause." Rarity replied. "I'm talking about hiding your stress and pain from me."

"I just can't come here every time and just spill on you what I had to deal with for the past three months." Alice replied.

Rarity finished stitching up the second gun shot wound Alice sustained from the fight as a courier came into the tent with an olive branch.

"An offering of peace?" Alice asked the courier as she shrugged her cloak on.

"Temporary, winter is coming up and our leaders suspect you don't want to fight during this time." The courier replied.

"Why would we trust you?" Alice asked him.

"So far you are the ones with the upper hand, having decimated our forces so far with only a single hundred lost on your side." The courier replied. "You have nothing to fear from us."

"It would be good, to have a break from all the war for awhile." Rarity replied.

Alice sighed as she got to two feet and lead the courier to the library where the other five of the assault group were already waiting.

"How?" The courier asked her.

"We knew you were coming." Alice replied as she shoved him into the center of the library. "Do you see those coffins right in front of you?"

The courier couldn't help but notice them as they were the focus of the whole place. The center tables were set around them and there were several books floating around them, flipping to random pages. Suddenly the library doors opened and Applejack slammed into Alice.

"How could you let them get killed?!" Applejack yelled as Rainbow Dash and Vinyl Scratch pulled her off of Alice.

"Who are they?" The courier asked them.

Alice who had been running a hoof through her mane suddenly stopped and the courier felt himself become weightless.

"You don't know who they are?" Alice asked him, her voice emotionless.

This by itself made everyone even Applejack back up as Alice floated upwards.

"Are you seriously this stupid?" Alice asked him. "They are the reason we fight, they were the casualties that started this war in the first place."

The courier gulped as Alice's voice started to seem to get more and more hollow with each word.

"Tell your leaders they can have their temporary treaty, but when this starts back up they will be destroyed." Alice told him as the library doors flew open. "I will storm your pitiful capital and destroy it making sure that there is _nothing_ left."

With that Alice dropped the courier to the ground and they galloped out of the library as Alice dropped to the ground in front of the coffins trying to choke back the same tears she felt every time she had when was near the coffins that held the bodies of Spike and Twilight Sparkle. This was the first time she let the tears come in front of her group; if she cried here with someone it was usually Rarity or Applebloom. Alice looked behind her to find that everyone was crying and she pulled Rarity close. Rarity had given up sewing beautiful dresses and fashion to stitching up wounds and repairing defensive clothing. Alice had come to know how Big Mac and Fluttershy felt as she wanted to tell Rarity how she felt about her and how she admired her strength and ability to keep working under what seemed to be the worst of circumstances; but she also didn't want to make her day to day any life harder then it already was, not only that she also didn't how Rarity felt able her. She didn't want Rarity to have to worry about whether she'd ever come back from one of the missions alive or in need to be put in a coffin.

"I don't want to have to see any more dead bodies." Rarity told her.

"We'll have a temporary shortage of the for awhile." Alice replied.

"For how long; a couple of weeks?" Rarity asked her. "This first week we'll all be mourning and burying the loved ones we lost, and then the second week won't be any better."

Rarity stopped as she noticed everyone staring at her everyone either sympathetic or empathetic but before she could run out of the library Alice pulled her close again. This time Rarity completely broke down and began to sob like a filly into Alice's chest who started to walk her out of the library, but Rarity stopped her before they left.

"Dash, t-tell me, w-when you are g-going to b-bury my s-sister." Rarity told her.

Rainbow Dash hugged her and Alice tightly before they left to Rarity's tent again.

When they got there Rarity and Alice collapsed on a pile of throw pillows that served as a temporary bed for them since they had to keep each other warm due to the dropping temperatures. Alice could still feel Rarity crying against her unscarred side and she draped a foreleg over her shoulders. She held her like that until her sobs turned into quiet sleeping whimpers. Alice laid her head next to Rarity's and somehow found nightmarish slumber. She woke up with a start as Rarity shook her.

"You were screaming again." Rarity replied sadly.

"I'm sorry that I woke you." Alice replied. "What does this make the count up to; 72 nights of nightmares?"

"I was already awake, when you started to scream I tried to comfort you, but you're a lot better at it." Rarity replied.

"Is it time?" Alice asked her.

All Rarity could was nod because she knew that if she spoke now that she cry herself out before the funeral even began. Alice hugged her tightly before they walked towards the center of town that had been turned into a cemetery. When Rarity saw the line of coffin and spotted the one with the initials S.B. she could barely hold back the tears. She saw Vinyl Scratch crying over a box with an O scratched into the side as Rainbow Dash rubbed her back and everything about the funeral procession blurred for her as she started to cry into Alice's shoulder. Alice knew she should say something, anything, but she couldn't leave Rarity at the moment and Rainbow Dash was preoccupied with Vinyl Scratch who was still holding tightly onto Octavia's coffin. Dr. Whooves stepped up but Alice was too focused on Rarity to notice what he was saying and when it was over she released a star for each coffin in the center. After all of this was over Rarity ended up crying on Sweetie Belle's coffin.


End file.
